Thread method

This section briefly reviews prediction of the native structure of a protein from its sequence of amino acid residues alone. These methods can be contrasted to the threading methods for fold assignment [Section II.A] [39-47,147], which detect remote relationships between sequences and folds of known structure, and to comparative modeling methods discussed in this review, which build a complete all-atom 3D model based on a related known structure. The methods for ab initio prediction include those that focus on the broad physical principles of the folding process [148-152] and the methods that focus on predicting the actual native structures of specific proteins [44,153,154,240]. The former frequently rely on extremely simplified generic models of proteins, generally do not aim to predict native structures of specific proteins, and are not reviewed here. 

Threading methods can assign amino acid sequences to known three-dimensional folds... 

Can one push the limits of the method so as to use models with less and less sequence identity with the target, i.e. models obtained by threading methods, with sequence identity levels between 15 and 25% The answer seems to be yes (Jones, 2001), with newer methods capable of solving problems with sequence identity around 20% (Claude et al., 2004 G. Labesse, personal commimication Abstract in the GTBio Meeting, June 2004, Lyon, France Keegan and Wynn, 2007). 

Elemans PHM, Janssen JMH and Meijer HEH (1990) The breaking thread method the measurement of interfacial tension in polymer systems. J Rheol 34 1311-22. 

Reddy et al. used a special method to calculate the differences in the solvation free energies for different molecules. The method was based on continuously transferring one (solute) molecule into the other using the so called thread method. Thus, when comparing the A molecule with the B molecule, they introduce a parameter X so that X- = 0 corresponds to the A molecule and A. = 1 to the B... 

Schoonman, M.J. Knegtel, R.M. Grootenhuis, P.D. Practical evaluation of comparative modelling and threading methods. Comput. Chem. 1998, 22 (5), 369-375. 

Structure-based methods are reviewed in [185] and can be classified into two types profile methods based on dynamic programming (see Chapter 2 of this volume) for computing optimal alignments of structural environments and threading approaches using full pair-interaction potentials [30, 125, 138, 186] (see Section 6.2). The latter methods use optimal exhaustive search procedures [175], branch and bound approximation algorithms [187, 188] or other heuristic approaches for the optimization [189, 190], Reviews and comparison of threading methods can be found in [186, 191, 192],... 

Profile threading methods As described in Section 6.2, algorithms that optimize threading profiles are the same as for pairwise sequence alignment and are based on dynamic programming. These methods have been introduced by Eisenberg et al. [136, 193, 194]. 

A detailed description and discussion can be found in [188]. The approach has been shown to improve on profile threading methods on several comprehensive benchmark sets containing structural pairs of increasing difficulty. 

Jones, D. T., et al., Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure. Proteins, 1999. 37(S3) p. 104-111. 

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